I thought this article in the NYTimes, "Economic Promises a President Trump Could (and Couldn’t) Keep, Much of what Donald Trump vows to accomplish in his first 100 days, if elected, is not feasible. But that doesn’t mean he wouldn’t have room to maneuver." was a good discussion of the influence of a President.
While the bureaucracy does restrain some of the impulses of the chief executive, her message can set the tone. As a further instance, I'd go back to the Reagan Administration and its handling of EEO in USDA. I'm sure Reagan didn't give orders, but his tone definitely said civil rights is not important in this administration. That IMHO set the stage for what happened in 1996-7, now known as the Pigford suit. Had the EEO machinery been kept in place and tuned up a bit, the problems of some of the lead plaintiffs in the suit might have been alleviated enough so there wouldn't have been the leadership to organize the lawsuit.